Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?
Hi Mark, Thank you for your help! Sorry I was totally confused. I thought I should delete the "define = -DPOSRES" option and use "-r target.pdb". Now I understand that. I should ) still keep the "define = -DPOSRES" in the mdp file ) still keep the "[ position_restraints ]" section in the itp file ) the only difference is, add "-r target.gro" where the "target.gro" can be the same as that for "-c" option. Thank you very much! Cheng -- Original -- From: "ZHANG Cheng"<272699...@qq.com>; Date: Wed, Jan 16, 2019 09:51 PM To: "gromacs.org_gmx-users"; Subject: What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018? My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to replace the "define = -DPOSRES" option in the .mdp file. However, how can I do position restraints only for certain atoms, e.g. only the backbone atoms? I think, if I use "-r target.pdb", both the backbone and side chain atoms in the "target.pdb" will be restrained. My coarse-grained pdb looks like this: ATOM 1 BB PRO A 1 -26.587 30.562 25.782 1.00 0.00 B ATOM 2 SC1 PRO A 1 -28.091 28.941 24.961 1.00 0.00 S ATOM 3 BB GLN A 2 -25.999 30.486 29.213 1.00 0.00 B ATOM 4 SC1 GLN A 2 -25.071 33.603 31.302 1.00 0.00 S ATOM 5 BB ILE A 3 -23.280 28.735 30.757 1.00 0.00 B ATOM 6 SC1 ILE A 3 -23.796 26.273 28.833 1.00 0.00 S ... ... ATOM201 BB ASN A 98 -16.655 34.258 30.350 1.00 0.00 B ATOM202 SC1 ASN A 98 -18.546 35.721 27.829 1.00 0.00 S ATOM203 BB PHE A 99 -15.212 36.640 33.153 1.00 0.00 B ATOM204 SC1 PHE A 99 -13.341 34.692 33.167 1.00 0.00 S ATOM205 SC2 PHE A 99 -11.471 35.716 34.112 1.00 0.00 S ATOM206 SC3 PHE A 99 -10.740 34.794 32.402 1.00 0.00 S The "position_restraints" looks like this in the protein.itp file: (you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, 203) #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC ... ... 2011POSRES_FCPOSRES_FCPOSRES_FC 2031POSRES_FCPOSRES_FCPOSRES_FC #endif -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?
Hi, Nothing has changed in the implementation. Atoms which have interactions specified have always had get position coordinates to target from somewhere. (Those atoms with no position restraint interactions never cared.) Historically the position coordinates came from the file you used for -c if you didn't use -r. Now you have to use -r, and you can give it the same file as for -c if you want the old behavior. That's what the grompp message says, right? Mark On Wed., 16 Jan. 2019, 14:52 ZHANG Cheng, <272699...@qq.com> wrote: > My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to > replace the "define = -DPOSRES" option in the .mdp file. > > > However, how can I do position restraints only for certain atoms, e.g. > only the backbone atoms? I think, if I use "-r target.pdb", both the > backbone and side chain atoms in the "target.pdb" will be restrained. > > > > > My coarse-grained pdb looks like this: > > > ATOM 1 BB PRO A 1 -26.587 30.562 25.782 1.00 0.00 >B > ATOM 2 SC1 PRO A 1 -28.091 28.941 24.961 1.00 0.00 >S > ATOM 3 BB GLN A 2 -25.999 30.486 29.213 1.00 0.00 >B > ATOM 4 SC1 GLN A 2 -25.071 33.603 31.302 1.00 0.00 >S > ATOM 5 BB ILE A 3 -23.280 28.735 30.757 1.00 0.00 >B > ATOM 6 SC1 ILE A 3 -23.796 26.273 28.833 1.00 0.00 >S > ... ... > ATOM201 BB ASN A 98 -16.655 34.258 30.350 1.00 0.00 >B > ATOM202 SC1 ASN A 98 -18.546 35.721 27.829 1.00 0.00 >S > ATOM203 BB PHE A 99 -15.212 36.640 33.153 1.00 0.00 >B > ATOM204 SC1 PHE A 99 -13.341 34.692 33.167 1.00 0.00 >S > ATOM205 SC2 PHE A 99 -11.471 35.716 34.112 1.00 0.00 >S > ATOM206 SC3 PHE A 99 -10.740 34.794 32.402 1.00 0.00 >S > > > > > > > > The "position_restraints" looks like this in the protein.itp file: > (you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, > 203) > > > #ifdef POSRES > #ifndef POSRES_FC > #define POSRES_FC 1000.00 > #endif > [ position_restraints ] > 11POSRES_FCPOSRES_FCPOSRES_FC > 31POSRES_FCPOSRES_FCPOSRES_FC > 51POSRES_FCPOSRES_FCPOSRES_FC > ... ... > 2011POSRES_FCPOSRES_FCPOSRES_FC > 2031POSRES_FCPOSRES_FCPOSRES_FC > #endif > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] What is the equivalent way to do postion restraints only for backbone atoms in Gromacs 2018?
My understanding is, in the Gromacs 2018, we MUST use "-r target.pdb" to replace the "define = -DPOSRES" option in the .mdp file. However, how can I do position restraints only for certain atoms, e.g. only the backbone atoms? I think, if I use "-r target.pdb", both the backbone and side chain atoms in the "target.pdb" will be restrained. My coarse-grained pdb looks like this: ATOM 1 BB PRO A 1 -26.587 30.562 25.782 1.00 0.00 B ATOM 2 SC1 PRO A 1 -28.091 28.941 24.961 1.00 0.00 S ATOM 3 BB GLN A 2 -25.999 30.486 29.213 1.00 0.00 B ATOM 4 SC1 GLN A 2 -25.071 33.603 31.302 1.00 0.00 S ATOM 5 BB ILE A 3 -23.280 28.735 30.757 1.00 0.00 B ATOM 6 SC1 ILE A 3 -23.796 26.273 28.833 1.00 0.00 S ... ... ATOM201 BB ASN A 98 -16.655 34.258 30.350 1.00 0.00 B ATOM202 SC1 ASN A 98 -18.546 35.721 27.829 1.00 0.00 S ATOM203 BB PHE A 99 -15.212 36.640 33.153 1.00 0.00 B ATOM204 SC1 PHE A 99 -13.341 34.692 33.167 1.00 0.00 S ATOM205 SC2 PHE A 99 -11.471 35.716 34.112 1.00 0.00 S ATOM206 SC3 PHE A 99 -10.740 34.794 32.402 1.00 0.00 S The "position_restraints" looks like this in the protein.itp file: (you can see only the backbone atom ID is listed, i.e. 1, 3, 5 ... 201, 203) #ifdef POSRES #ifndef POSRES_FC #define POSRES_FC 1000.00 #endif [ position_restraints ] 11POSRES_FCPOSRES_FCPOSRES_FC 31POSRES_FCPOSRES_FCPOSRES_FC 51POSRES_FCPOSRES_FCPOSRES_FC ... ... 2011POSRES_FCPOSRES_FCPOSRES_FC 2031POSRES_FCPOSRES_FCPOSRES_FC #endif -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
